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Series GSE119396 Query DataSets for GSE119396
Status Public on Jun 18, 2019
Title Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2 [ATAC-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Oct4, along with Sox2 and Klf4 (SK), can induce pluripotency but structurally similar factors like Oct6 cannot. To decode why Oct4 has this unique ability, we compare Oct4-binding, accessibility patterns and transcriptional waves with Oct6 and an Oct4 mutant defective in the dimerization with Sox2 (Oct4defSox2). We find that initial silencing of the somatic program proceeds indistinguishably with or without Oct4. Oct6 mitigates the mesenchymal-to-epithelial transition and derails reprogramming. These effects are a consequence of differences in genome-wide binding, as the early binding profile of Oct4defSox2 resembles Oct4, whilst Oct6 does not bind pluripotency enhancers. Nevertheless, in the Oct6-SK condition many otherwise Oct4-bound locations become accessible but chromatin opening is compromised when Oct4defSox2 occupies these sites. We find that Sox2 predominantly facilitates chromatin opening, whilst Oct4 serves an accessory role. Formation of Oct4/Sox2 heterodimers is essential for pluripotency establishment; however, reliance on Oct4/Sox2 heterodimers declines during pluripotency maintenance.
Overall design We analyzed the chromatin accessibility profiles of Oct4,Oct6 and an Oct4 mutant with two interface mutations leading to a disruption of the DNA dependent dimer with Sox2 (Oct4I21Y/D29R in manuscript termed Oct4defSox2 and data in GEO is submitted by name “YR”) in replicates at days 1 and 5 of retrovirus based somatic cell reprogramming to iPSC in highly efficient chemically defined iCD1 medium
Contributor(s) Malik V, Veerapandian V, Jauch R
Citation(s) 31375664
Submission date Sep 04, 2018
Last update date Aug 20, 2019
Contact name Veeramohan Veerapandian
Organization name Max Planck Institute for Molecular Biomedicine
Department Department Tissue Morphogenesis
Street address Röntgenstr. 20
City Munster
State/province North Rhine-Westphalia
ZIP/Postal code 48149
Country Germany
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (12)
GSM3374129 O4SK_d1_rep1ATAC
GSM3374130 O4SK_d1_rep2ATAC
GSM3374131 O4SK_d5_rep1ATAC
This SubSeries is part of SuperSeries:
GSE103980 Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2
BioProject PRJNA489174
SRA SRP159491

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Supplementary file Size Download File type/resource
GSE119396_RAW.tar 3.3 Gb (http)(custom) TAR (of BW, NARROWPEAK)
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Raw data are available in SRA
Processed data provided as supplementary file

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